Denotes: *equal author contribution; ^corresponding author; Dennis lab members in bold

Preprints

The complete sequence of a human genome.

Nurk S*, Koren S*, Rhie A*, Rautiainen M*, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Cheng H, Chin C, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, SchneiderVA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O’Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE^, Miga KH^, Phillippy AM^. bioRxiv. 2021. doi: 10.1101/2021.05.26.445798. [Telomere-to-Telomere Consortium github][UCSC Genome Browser CHM13 hub]

Evaluation of CRISPR gene-editing tools in zebrafish.

Uribe-Salazar JM, Sekar A, Kaya Gulhan, Weyenberg KB, Ingamells C, Dennis MY^. bioRxiv. 2021. doi: 10.1101/2020.10.19.345256.

2021

Diverse molecular mechanisms contribute to differential expression of human duplicated genes.

Shew CJ, Carmona-Mora P, Soto DC, Mastoras M, Roberts E, Rosas J, Jagannathan D, Kaya G, O’Geen H, Dennis MY^. MBE. 2021. [ChIP-seq data analysis snakemake] [UCSC track hub] [Data available at ENA]

2020

Assessment of autism zebrafish mutant models using a high-throughput larval phenotyping platform.

Colón-Rodríguez A, Uribe-Salazar JM, Weyenberg KB, Sriram A, Quezada A, Kaya G, Jao E, Radke B, Lein PJ, Dennis MY^. Front Cell Dev Biol: Zebrafish Models for Human Disease Studies. 2020 Nov 23. [Data available on github][Data available on ENA]

Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution.

Maggiolini FAM, Sanders AD, Shew CJ, Sulovari A, Mao Y, Puig M, Catacchio CR, Dellino M, Palmisano D, Mercuri L, Bitonto M, Porubský D, Cáceres M, Eichler EE, Ventura M, Dennis MY, Korbel JO, Antonacci F^. Genome Res. 2020 Oct 22. [Rhesus Hi-C data available at ENA]

Telomere-to-telomere assembly of a complete human X chromosome.

Miga KH*^, Koren S*, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques RA, Lindsay TAG, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM^. Nature. Jul 14. 2020.

Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing.

Soto DC*, Shew C*, Mastoras M, Schmidt JM, Sahasrabudhe R, Kaya G, Andrés AM, Dennis MY^. Genes (Basel). 2020 Mar 4;11(3). [Data available on github][Data available at ENA]

2018

Psychedelics Promote Structural and Functional Neural Plasticity.

Ly C, Greb AC,Cameron LP, Wong JM, Barragan EV, Wilson PC, Burbach KF, Zarandi SS, Sood A, Paddy MR, Duim WC, Dennis MY, McAllister AK, Ori-McKenney KM, Gray JA, Olson DE^. Cell Reports. 2018.

Human local adaptation of the TRPM8 cold receptor along a latitudinal cline.

Key FM, Abdul-Aziz MA, Mundry R, Peter B, Sekar A, Amato MD, Dennis MY, Schmidt JM, Andres AM^. PLOS Genet. 2018 May 3;14(5):e1007298.

2017

The birth of a human-specific neural gene by incomplete duplication and gene fusion.

Dougherty ML*, Nuttle X*, Penn O, Nelson BJ, Huddleston J, Baker C, Harshman L, Duyzend MH, Ventura M, Antonacci F, Sandstrom R, Dennis MY, Eichler EE^. Genome Biology. 2017; 18(1):49.

The evolution and population diversity of human-specific segmental duplications.

Dennis MY, Harshman L, Nelson BJ, Penn O, Cantsilieris S, Huddleston J, Antonacci F, Penewit K, Denman L, Raja A, Baker C, Mark K, Malig M, Janke N, Espinoza C, Stessman HA, Nuttle X, Hoekzema K, Graves TA, Wilson RK, Eichler EE^. Nat Ecol Evol. 2017 Mar. [Supplementary Information] [Supplementary Tables] [Supplementary Data][1KG data available at NCBI]

2016

Human adaptation and evolution by segmental duplication.

Dennis MY and Eichler EE^. Curr Opin Genet Dev. 2016 Dec; 41:44–52

2011-2015

Epigenetics of autism-related impairment: Copy number variation and maternal infection.

Mazina V, Gerdts J, Ankenman K, Ward T, Dennis MY, Girirajan S, Eichler EE^, and Bernier R^. JDBP. 2015 Feb-Mar;36(2):61-7.

Resolving the complexity of the human genome using single-molecule sequencing.

Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M, Landolin J, Stamatoyannopoulos JA, Hunkapiller MW, Korlach J, Eichler EE^. Nature. 2015 Jan 29;517(7536):608-11.

Palindromic GOLGA8 core duplicons promote 15q13.3 microdeletion and evolutionary instability.

Antonacci F*, Dennis MY*, Huddleston J, Sudmant PH, Meltz Steinberg K, Graves TA, Vives L, Malig M, Denman L, Baker C, Amemiya CT, Stuart A, Tang J, Muson B, Rosenfeld JA, Shaffer LG, Wilson RK, and Eichler EE^. Nat Genet. 2014 Dec;46(12):1293-302. 

Selection on a variant associated with improved viral clearance induced local, adaptive pseudogenization of interferon lambda 4 (IFNL4).

Key FM, Peter B, Dennis MY, Huerta-Sanchez E, Tang W, Nielsen R, Prokunina-Olsson L, and Andres AM^. 2014. PLOS Genet 10(10):e1004681.

Reconstructing complex regions of genomes using long-read sequencing technology.

Huddleston JH, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, Sudmant PH, Graves TA, Alkan C, Dennis MY, Wilson RK, Turner SW, Korlach J, and Eichler EE^. 2014. Genome Res 24(4):688-96.

Refinement and discovery of new hotspots of copy number variation associated with autism spectrum disorder.

Girirajan S*, Dennis MY*, Baker C, Malig M, Coe BP, Campbell CD, Mark K, Vu TH, Alkan C, Cheng Z, Biesecker LG, Bernier R, and Eichler EE^. 2013. AJHG 92(2):221-37.

Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication.

Dennis MY*, Nuttle X*, Sudmant PH, Antonacci F, Graves TA, Nefedov M, Rosenfeld JA, Sajjadian S, Malig M, Kotkiewicz H, Curry CJ, Shafer S, Shaffer LG, de Jong PJ, Wilson RK, and Eichler EE^. 2012. Cell 149(4):912-22.

Detection of structural variants and indels within exome data.

Karakoc E, Alkan C, O'Roak BJ, Dennis MY, Vives L, Mark K, Rieder MJ, Nickerson DA, and Eichler EE^. 2011. Nat Methods 9(2):176-8.

2010 and before

A rare myelin protein zero (MPZ) variant alters enhancer activity in vitro and in vivo.

Antonellis A*, Dennis MY*, Burzynski G, Huynh J, Maduro V, Khajavi M, Szigeti K, Mukkamala S, Bessling SL, NISC Comparative Sequencing Program, McCallion AS, Pavan WJ, Lupski JR, and Green ED^. 2010. PLOS One 5(12):e14346.

Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation.

Andres AM*^, Dennis MY*, Kretzschmar W, Cannons JL, Lee-Lin S, Hurle B, NISC Comparative Sequencing Program, Schwartzberg PL, Williamson S, Bustamante CD, Nielsen R, Clark AG, and Green ED^. 2010. PLOS Genet 6(10): e1001157.

A common variant associated with dyslexia reduces expression of the KIAA0319 gene.

2009. Dennis MY, Paracchini S, Scerri TS, Prokunina-Olsson L, Knight JC, Wade-Martins R, Coggill P, Beck S, Green ED^, and Monaco AP^. PLOS Genet 5(3): e1000436.

Further evidence that the KIAA0319 gene confers susceptibility to developmental dyslexia.

Harold D*, Paracchini S*, Scerri T, Dennis M, Cope N, Hill G, Moskvina V, Walter J, Richardson AJ, Owen MJ, Stein JF, Green ED, O'Donovan MC, Williams J, Monaco AP^. 2006. Mol Psychiatry 11, 1085-1091, 1061.

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